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Journal articles on the topic 'Population genetic connectivity'
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1
Putri, S. N. N., G. R. Maharani, M. Farhan, D. F. Lestari, H. Madduppa, B. Subhan, D. Arafat, et al. "Population connectivity and genetic diversity population connectivity of Rabbitfish (Siganus canaliculatus) among Bangladesh, China and Indonesia." IOP Conference Series: Earth and Environmental Science 1033, no. 1 (June 1, 2022): 012043. http://dx.doi.org/10.1088/1755-1315/1033/1/012043.
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Abstract Population genetics studies genetic variation involving gene and allele frequencies in spatial and temporal space. Genetic information can be used in conservation management through identification of phylogenetic tree reconstructions, genetic distance, genetic structure, and haplotype connectivity to maintain population existence. The samples used were primary genetic data of Siganus canaliculatus taken from Indonesian waters and secondary data accessed from the BOLD SYSTEM database from several locations, namely Indonesia, China, and Bangladesh. This research was conducted to determine the kinship of Siganus canaliculatus in Indonesia, China, and Bangladesh through genetic analysis. The results of genetic distance analysis showed that the baronang fish samples from China and Bangladesh had a close relationship with a value of 0.0534 while samples from Indonesia and Bangladesh had the farthest relationship with a value of 0.8212. Reconstruction of the phylogeny tree at maximum likelihood can show convergence within the same clade. The results of the reconstruction of the phylogeny tree showed that the species from Ambon, Bali, and Lombok came from the same clade while samples from Bangladesh had different clades with the furthest distance. The results of structural analysis and genetic diversity showed that samples from Bangladesh, China, and Indonesia had different DNA characteristics. This is correlated with the form of network integration in haplotype connectivity analysis.
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Marandel, Florianne, Pascal Lorance, Marco Andrello, Grégory Charrier, Sabrina Le Cam, Sigrid Lehuta, and Verena M. Trenkel. "Insights from genetic and demographic connectivity for the management of rays and skates." Canadian Journal of Fisheries and Aquatic Sciences 75, no. 8 (August 2018): 1291–302. http://dx.doi.org/10.1139/cjfas-2017-0291.
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Studying demographic and genetic connectivity can help assess marine metapopulation structure. Rays and skates have no larval phase; hence, population connectivity can only result from active movement of individuals. Using thornback ray (Raja clavata) in European waters as a case study, demographic and genetic connectivity were studied for 11 putative populations with unequal population abundances and two hypotheses of dispersal rates. Genetic simulation results highlighted three large metapopulations: in the Mediterranean, around the Azores, and on the Northeast Atlantic shelf. Demographic results highlighted a finer population structure indicating that several pairs of putative populations might be demographically linked. Results were highly sensitive to dispersal assumptions and relative population abundances, which provided insights into the potential magnitude of genetic and demographic connectivity differences. Accounting for demographic connectivity appears to be crucial for managing and conserving rays and skates, while genetic connectivity provides a longer-term perspective and less subtle spatial structures. Moreover, accounting for heterogeneity in population abundances is a key factor for determining or interpreting metapopulation connectivity.
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Jangjoo, Maryam, Stephen F. Matter, Jens Roland, and Nusha Keyghobadi. "Connectivity rescues genetic diversity after a demographic bottleneck in a butterfly population network." Proceedings of the National Academy of Sciences 113, no. 39 (September 12, 2016): 10914–19. http://dx.doi.org/10.1073/pnas.1600865113.
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Demographic bottlenecks that occur when populations fluctuate in size erode genetic diversity, but that diversity can be recovered through immigration. Connectivity among populations and habitat patches in the landscape enhances immigration and should in turn facilitate recovery of genetic diversity after a sudden reduction in population size. For the conservation of genetic diversity, it may therefore be particularly important to maintain connectivity in the face of factors that increase demographic instability, such as climate change. However, a direct link between connectivity and recovery of genetic diversity after a demographic bottleneck has not been clearly demonstrated in an empirical system. Here, we show that connectivity of habitat patches in the landscape contributes to the maintenance of genetic diversity after a demographic bottleneck. We were able to monitor genetic diversity in a network of populations of the alpine butterfly, Parnassius smintheus, before, during, and after a severe reduction in population size that lasted two generations. We found that allelic diversity in the network declined after the demographic bottleneck but that less allelic diversity was lost from populations occupying habitat patches with higher connectivity. Furthermore, the effect of connectivity on allelic diversity was important during the demographic recovery phase. Our results demonstrate directly the ability of connectivity to mediate the rescue of genetic diversity in a natural system.
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Caplins, Serena A., Kimberly J. Gilbert, Claudia Ciotir, Jens Roland, Stephen F. Matter, and Nusha Keyghobadi. "Landscape structure and the genetic effects of a population collapse." Proceedings of the Royal Society B: Biological Sciences 281, no. 1796 (December 7, 2014): 20141798. http://dx.doi.org/10.1098/rspb.2014.1798.
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Both landscape structure and population size fluctuations influence population genetics. While independent effects of these factors on genetic patterns and processes are well studied, a key challenge is to understand their interaction, as populations are simultaneously exposed to habitat fragmentation and climatic changes that increase variability in population size. In a population network of an alpine butterfly, abundance declined 60–100% in 2003 because of low over-winter survival. Across the network, mean microsatellite genetic diversity did not change. However, patch connectivity and local severity of the collapse interacted to determine allelic richness change within populations, indicating that patch connectivity can mediate genetic response to a demographic collapse. The collapse strongly affected spatial genetic structure, leading to a breakdown of isolation-by-distance and loss of landscape genetic pattern. Our study reveals important interactions between landscape structure and temporal demographic variability on the genetic diversity and genetic differentiation of populations. Projected future changes to both landscape and climate may lead to loss of genetic variability from the studied populations, and selection acting on adaptive variation will likely occur within the context of an increasing influence of genetic drift.
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Padrón, Mariana, and Katell Guizien. "Modelling the effect of demographic traits and connectivity on the genetic structuration of marine metapopulations of sedentary benthic invertebrates." ICES Journal of Marine Science 73, no. 7 (September 8, 2015): 1935–45. http://dx.doi.org/10.1093/icesjms/fsv158.
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Abstract Accounting for connectivity is essential in marine spatial planning and the proper design and management of marine protected areas, given that their effectiveness depends on the patterns of dispersal and colonization between protected and non-protected areas. The genetic structure of populations is commonly used to infer connectivity among distant populations. Here, we explore how population genetic structure is affected by pre- and settlement limitations with a spatially explicit coupled metapopulation-gene flow model that simulates the effect of demographic fluctuations on the allele frequencies of a set of populations. We show that in closed populations, regardless of population growth rate, the maintenance of genetic diversity at saturating initial population density increases with species life expectancy as a result of density-dependent recruitment control. Correlatively, at low initial population density, the time at which a population begins to lose its genetic diversity is driven larval and post-settlement mortality (comprised in the recruitment success parameter)—the larger the recruitment success, the stronger the genetic drift. Different spatial structures of connectivity established for soft bottom benthic invertebrates in the Gulf of Lions (NW Mediterranean, France) lead to very different results in the spatial patterns of genetic structuration of the metapopulation, with high genetic drift in sites where the local retention rate was larger than 2%. The effect of recruitment failure and the loss of key source populations on heterozygosity confirm that transient demographic fluctuations help maintain genetic diversity in a metapopulation. This study highlights the role of intraspecific settlement limitations due to lack of space when the effective number of breeders approaches saturating capacity, causing a strong reduction in effective reproduction. The present model allows to: (i) disentangle the relative contribution of local demography and environmental connectivity in shaping seascape genetics, and (ii) perform in silico evaluations of different scenarios for marine spatial planning.
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Weckworth, Byron V., Marco Musiani, Nicholas J. DeCesare, Allan D. McDevitt, Mark Hebblewhite, and Stefano Mariani. "Preferred habitat and effective population size drive landscape genetic patterns in an endangered species." Proceedings of the Royal Society B: Biological Sciences 280, no. 1769 (October 22, 2013): 20131756. http://dx.doi.org/10.1098/rspb.2013.1756.
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Landscape genetics provides a framework for pinpointing environmental features that determine the important exchange of migrants among populations. These studies usually test the significance of environmental variables on gene flow, yet ignore one fundamental driver of genetic variation in small populations, effective population size, N e . We combined both approaches in evaluating genetic connectivity of a threatened ungulate, woodland caribou. We used least-cost paths to calculate matrices of resistance distance for landscape variables (preferred habitat, anthropogenic features and predation risk) and population-pairwise harmonic means of N e , and correlated them with genetic distances, F ST and D c . Results showed that spatial configuration of preferred habitat and N e were the two best predictors of genetic relationships. Additionally, controlling for the effect of N e increased the strength of correlations of environmental variables with genetic distance, highlighting the significant underlying effect of N e in modulating genetic drift and perceived spatial connectivity. We therefore have provided empirical support to emphasize preventing increased habitat loss and promoting population growth to ensure metapopulation viability.
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Campos, João Carlos, Asghar Mobaraki, Elham Abtin, Raquel Godinho, and José Carlos Brito. "Preliminary assessment of genetic diversity and population connectivity of the Mugger Crocodile in Iran." Amphibia-Reptilia 39, no. 1 (2018): 126–31. http://dx.doi.org/10.1163/15685381-16000173.
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The Mugger Crocodile (Crocodylus palustris) is a threatened reptile inhabiting the Indian Sub-continent and Western Asia. Despite its “Vulnerable” conservation status, data about population genetic structure and connectivity are unavailable. This study makes a preliminary assessment of the genetic diversity, population structure and habitat connectivity ofC. palustrisin Iran. Ten tissue samples collected along the Sarbaz-Bahukalat basins were analysed and a set of 12 microsatellites was genotyped. Genetic diversity indices were estimated and population substructuring was assessed through Bayesian clustering analysis. Potential connectivity was verified through Remote Sensing water indexes, further implemented in a circuit analysis. Low genetic diversity was observed (mean observed heterozygosity = 0.35; mean expected heterozygosity = 0.43) and no population structure was found (K = 1). Water index and circuit analysis suggested possible connection among sites. This study highlights the potential vulnerability of crocodile populations and the importance of habitat connectivity for their persistence in the arid regions of Iran.
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Eschenroeder, Jackman C., and James H. Roberts. "Habitat loss, fragmentation, and the genetic status of Roanoke bass." Canadian Journal of Fisheries and Aquatic Sciences 77, no. 2 (February 2020): 375–87. http://dx.doi.org/10.1139/cjfas-2019-0103.
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Roanoke bass (Ambloplites cavifrons) persist in five river basins in the eastern US, where they are threatened by invasive species, habitat loss and degradation, and hydrologic fragmentation. We conducted the first conservation genetic study of A. cavifrons, analyzing variation at 19 nuclear microsatellite DNA loci and the cytochrome b mitochondrial DNA gene to estimate population structure and demography, genetic relationships among populations, and the role of landscape features in regulating genetic diversity and differentiation. Most streams harbored genetically distinguishable populations, with high connectivity among reaches within streams but no contemporary dispersal among streams. In contrast, mitochondrial divergence within and among basins was weak, suggesting historically higher range-wide connectivity. Most populations exhibited small effective population sizes and evidence of past population bottlenecks. Genetic diversity correlated positively with patch size but negatively with watershed urban and agricultural development, suggesting that habitat loss, degradation, and fragmentation have acted in concert to reduce population viability. Mitigating these impacts may require a combination of tactics, including restoring habitat, limiting the spread of invasive competitors, and reestablishing historical connectivity.
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Douglas, Marlis R., Steven M. Mussmann, Tyler K. Chafin, Whitney J. B. Anthonysamy, Mark A. Davis, Matthew P. Mulligan, Robert L. Schooley, Wade Louis, and Michael E. Douglas. "Population connectivity in voles (Microtus sp.) as a gauge for tall grass prairie restoration in midwestern North America." PLOS ONE 16, no. 12 (December 9, 2021): e0260344. http://dx.doi.org/10.1371/journal.pone.0260344.
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Ecological restoration can promote biodiversity conservation in anthropogenically fragmented habitats, but effectiveness of these management efforts need to be statistically validated to determine ’success.’ One such approach is to gauge the extent of recolonization as a measure of landscape permeability and, in turn, population connectivity. In this context, we estimated dispersal and population connectivity in prairie vole (Microtus ochrogaster; N = 231) and meadow vole (M. pennsylvanicus; N = 83) within five tall-grass prairie restoration sites embedded within the agricultural matrix of midwestern North America. We predicted that vole dispersal would be constrained by the extent of agricultural land surrounding restored habitat patches, spatially isolating vole populations and resulting in significant genetic structure. We first employed genetic assignment tests based on 15 microsatellite DNA loci to validate field-derived species-designations, then tested reclassified samples with multivariate and Bayesian clustering to assay for spatial and temporal genetic structure. Population connectivity was further evaluated by calculating pairwise FST, then potential demographic effects explored by computing migration rates, effective population size (Ne), and average relatedness (r). Genetic species assignments reclassified 25% of initial field identifications (N = 11 M. ochrogaster; N = 67 M. pennsylvanicus). In M. ochrogaster population connectivity was high across the study area, reflected in little to no spatial or temporal genetic structure. In M. pennsylvanicus genetic structure was detected, but relatedness estimates identified it as kin-clustering instead, underscoring social behavior among populations rather than spatial isolation as the cause. Estimates of Ne and r were stable across years, reflecting high dispersal and demographic resilience. Combined, these metrics suggest the agricultural matrix is highly permeable for voles and does not impede dispersal. High connectivity observed confirms that the restored landscape is productive and permeable for specific management targets such as voles and also demonstrates population genetic assays as a tool to statistically evaluate effectiveness of conservation initiatives.
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Stafford-Bell, R. E., W. F. D. van Dongen, R. W. Robinson, and A. A. Chariton. "Connectivity of the seagrass Zostera muelleri within south-eastern Australia." Marine and Freshwater Research 70, no. 8 (2019): 1056. http://dx.doi.org/10.1071/mf18333.
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Contemporary oceanic conditions and local dispersal of propagules influence the genetic diversity and connectivity among seagrass populations. The degree of connectivity between populations of Zostera muelleri in south-eastern Australia is unknown. In this study we examined genetic connectivity among 25 sites containing Z. muelleri using nine polymorphic microsatellite DNA loci. We hypothesised minimal sharing of genetic material between distant populations and a degree of connectivity between local populations. Genotypic diversity was high, with 64% of populations having unique multilocus genotypes (MLGs), indicating the importance of sexual reproduction. Two sites shared MLGs, which may be due to the dispersal and recruitment of vegetative propagules. Genetic differentiation was observed between most sites. With the exception of two outlying sites, two genetic population clusters were identified across the studied populations. Regionally, the populations have high clonal diversity, are strongly differentiated and generally exist in isolation from one another. However, non-significant within-estuary differentiation was observed for three estuaries, indicating a degree of connectivity. The results of this research improve our understanding of the connectivity of Z. muelleri populations in the region, an important process for managing this ecosystem engineer.
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Ross, Steven, Jean-Marc Costanzi, Mansoor Al Jahdhami, Haitham Al Rawahi, Muhammad Ghazali, and Helen Senn. "First evaluation of the population structure, genetic diversity and landscape connectivity of the Endangered Arabian tahr." Mammalian Biology 100, no. 6 (October 13, 2020): 659–73. http://dx.doi.org/10.1007/s42991-020-00072-4.
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AbstractThe Arabian tahr (Arabitragus jayakari) occurs only in the mountains of northern Oman and the United Arab Emirates. The species is classified as Endangered due to its small declining population. In this study, we combined genetic and landscape ecology techniques in order to inform landscape scale conservation and genetic management of Arabian tahr. Using 540 base pairs of mitochondrial control region in a dataset of 53 samples, we found eight haplotypes, which fell into two haplogroups. Population genetic analysis using a panel of 14 microsatellite loci also showed a weak, but significant division. Analyses of landscape connectivity supported the genetic results showing poor connectivity between populations in the far south of the study area and those in the north. The most likely location of corridors connecting Arabian tahr populations were identified. Many corridors between tahr populations are impeded by multi-lane highways and restoration of these connections is required to maintain population viability of Arabian tahr. Owing to limited genetic samples outside of Wadi Sareen, further sampling is needed to elucidate both mtDNA and the nuclear structure of Arabian tahr more fully. Our study provides a toolkit that may be used for future genetic and connectivity monitoring of the Arabian tahr population.
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Schulwitz, Sarah, Jeff Johnson, and Bryan Bedrosian. "Low Neutral Genetic Diversity in an Isolated Greater Sage Grouse (Centrocercus Urophasianus) Population in Northwest Wyoming." UW National Parks Service Research Station Annual Reports 35 (January 1, 2012): 119–33. http://dx.doi.org/10.13001/uwnpsrc.2012.3943.
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Habitat loss is well recognized as an immediate threat to biodiversity. Depending on the dispersal capabilities of the species, increased habitat fragmentation often results in reduced functional connectivity and gene flow followed by population decline and a higher likelihood of eventual extinction. Knowledge of the degree of connectivity between populations is therefore crucial for better management of small populations in a changing landscape. A small population of greater sage-grouse (Centrocercus urophasianus) exists in northwest Wyoming within the Jackson Hole valley, including Grand Teton National Park and the National Elk Refuge. To what degree the Jackson population is isolated is not known as natural dispersal barriers in the form of mountains and anthropogenic habitat fragmentation may limit the populationâs connectivity to adjacent populations. Using 16 microsatellite loci and 300 greater sage-grouse samples collected throughout Wyoming and southeast Montana, significant population differentiation was found to exist among populations. Results indicated that the Jackson population was isolated relative to the other sampled populations, including Pinedale, its closest neighboring large population to the south. The one exception was a small population immediately to the east of Jackson, in which asymmetric dispersal from Jackson into Gros Ventre was detected. Both Jackson and Gros Ventre populations exhibited significantly reduced levels of neutral genetic diversity relative to other sampled populations. More work is warranted to determine the timing at which Jackson and Gros Ventre populations had become isolated and whether it was primarily due to recent habitat fragmentation or more historic processes. Due to its small population size, continual monitoring of the population is recommended with the goal of at least maintaining current population size and, if possible, increasing suitable habitat and population size to levels recorded in the past.
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Hansen, Heidi, Steven C. Hess, David Cole, and Paul C. Banko. "Using population genetic tools to develop a control strategy for feral cats (Felis catus) in Hawai'i." Wildlife Research 34, no. 8 (2007): 587. http://dx.doi.org/10.1071/wr07043.
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Population genetics can provide information about the demographics and dynamics of invasive species that is beneficial for developing effective control strategies. We studied the population genetics of feral cats on Hawai‘i Island by microsatellite analysis to evaluate genetic diversity and population structure, assess gene flow and connectivity among three populations, identify potential source populations, characterise population dynamics, and evaluate sex-biased dispersal. High genetic diversity, low structure, and high number of migrants per generation supported high gene flow that was not limited spatially. Migration rates revealed that most migration occurred out of West Mauna Kea. Effective population size estimates indicated increasing cat populations despite control efforts. Despite high gene flow, relatedness estimates declined significantly with increased geographic distance and Bayesian assignment tests revealed the presence of three population clusters. Genetic structure and relatedness estimates indicated male-biased dispersal, primarily from Mauna Kea, suggesting that this population should be targeted for control. However, recolonisation seems likely, given the great dispersal ability that may not be inhibited by barriers such as lava flows. Genetic monitoring will be necessary to assess the effectiveness of future control efforts. Management of other invasive species may benefit by employing these population genetic tools.
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Kingsford, Michael J., Jodie A. Schlaefer, and Scott J. Morrissey. "Population Structures and Levels of Connectivity for Scyphozoan and Cubozoan Jellyfish." Diversity 13, no. 4 (April 19, 2021): 174. http://dx.doi.org/10.3390/d13040174.
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Understanding the hierarchy of populations from the scale of metapopulations to mesopopulations and member local populations is fundamental to understanding the population dynamics of any species. Jellyfish by definition are planktonic and it would be assumed that connectivity would be high among local populations, and that populations would minimally vary in both ecological and genetic clade-level differences over broad spatial scales (i.e., hundreds to thousands of km). Although data exists on the connectivity of scyphozoan jellyfish, there are few data on cubozoans. Cubozoans are capable swimmers and have more complex and sophisticated visual abilities than scyphozoans. We predict, therefore, that cubozoans have the potential to have finer spatial scale differences in population structure than their relatives, the scyphozoans. Here we review the data available on the population structures of scyphozoans and what is known about cubozoans. The evidence from realized connectivity and estimates of potential connectivity for scyphozoans indicates the following. Some jellyfish taxa have a large metapopulation and very large stocks (>1000 s of km), while others have clade-level differences on the scale of tens of km. Data on distributions, genetics of medusa and polyps, statolith shape, elemental chemistry of statoliths and biophysical modelling of connectivity suggest that some of the ~50 species of cubozoans have populations of surprisingly small spatial scales and low levels of connectivity. Despite their classification as plankton, therefore, some scyphozoans and cubozoans have stocks of small spatial scales. Causal factors that influence the population structure in many taxa include the distribution of polyps, behavior of medusa, local geomorphology and hydrodynamics. Finally, the resolution of patterns of connectivity and population structures will be greatest when multiple methods are used.
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Drake, Christine C., Micheline Manseau, Cornelya F. C. Klütsch, Pauline Priadka, Paul J. Wilson, Steve Kingston, and Natasha Carr. "Does connectivity exist for remnant boreal caribou (Rangifer tarandus caribou) along the Lake Superior Coastal Range? Options for landscape restoration." Rangifer 38, no. 1 (January 19, 2018): 13–26. http://dx.doi.org/10.7557/2.38.1.4124.
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Genetic analysis can provide important information on the dynamic and spatial structure of groups of animals or populations. Little is known of the genetic population structure of caribou that inhabit the Lake Superior Coastal Range (LSCR) and the level of gene flow between individuals within the range and beyond. From a landscape perspective, this range is spatially isolated and genetic connectivity within the range is presumed limited due to large water crossings on Lake Superior. This study aims to answer if animal movement can be discerned, using genetic population and relatedness analyses, within and beyond the LSCR. Faecal and hair samples collected between 2005 and 2015 in Pukaskwa National Park were analyzed for genetic markers and compared to 131 unique genotypes previously obtained from both within the LSCR and in the two next closest ranges. Animals from one nearshore island (i.e. Otter) were more closely associated with offshore islands than other mainland caribou, likely a result of past movement and translocation rather than ongoing movement. Conversely, on another nearshore island (i.e. Pic), individuals assigned to a different genetic cluster and were related to animals further north outside the range, demonstrating some connectivity through the discontinuous distribution to the coast. Long-term population declines have been observed in the LSCR range despite genetic connectivity within the range and relatively low total habitat disturbance. Restoring connectivity of the LSCR so that it is not isolated from populations to the north is required for the recovery of the mainland portion of the coastal range. These genetic analyses provide some insights on where movements may occur and where landscape restoration efforts may best be directed to enhance connectivity.
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Digiantonio, Gina, Linda Blum, Karen McGlathery, Kor-jent van Dijk, and Michelle Waycott. "Genetic mosaicism and population connectivity of edge-of-range Halodule wrightii populations." Aquatic Botany 161 (February 2020): 103161. http://dx.doi.org/10.1016/j.aquabot.2019.103161.
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Liao, Te-Yu, Pei-Luen Lu, Yuan-Huan Yu, Wen-Chien Huang, Jen-Chieh Shiao, Hung-Du Lin, Wei-Cheng Jhuang, Tak-Kei Chou, and Fan Li. "Amphidromous but endemic: Population connectivity of Rhinogobius gigas (Teleostei: Gobioidei)." PLOS ONE 16, no. 2 (February 11, 2021): e0246406. http://dx.doi.org/10.1371/journal.pone.0246406.
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Rhinogobius gigas is an amphidromous fish endemic to eastern Taiwan. Fishes with the diadromous behavior are expected to have a broader distribution range and higher genetic homogeneity despite that some amphidromous fishes with limited distribution are observed and R. gigas is an additional exception with a limited distribution range. Rhinogobius gigas has been documented to be retained inshore near the river plume with a short pelagic larval duration of 30–40 days, which may account for the endemism of this species. The short marine larval stage of R. gigas may imply a population genetic structure and the aim of the present study is to test whether the population genetic structure is present in R. gigas. To test the population genetic structure, fragments of mitochondrial displacement loop and cytochrome c oxidase subunit I were sequenced to provide molecular inference for genetic structure among populations. Sixty-nine haplotypes were identified among 191 R. gigas from 10 populations of eastern Taiwan and the mean haplotype and nucleotide diversities for all samples were 0.956 and 0.0024, respectively, implying a bottleneck followed by a recent population expansion further supported by Fu’s Fs (-26.6; p < 0.001) and Tajima’s D (-1.5; p = 0.037) values. The phylogenetic analysis revealed lack of genetic structure and the bush-like median joining network without commonly shared haplotypes supports the same scenario. The genetic homogeneity is probably due to the amphidromous life history providing the opportunity for passive larval transportation among the rivers through coastal currents in eastern Taiwan. The endemism to eastern Taiwan may be a consequence of complicated interactions among short pelagic larval duration, interspecific competition and coastal currents.
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Veale, A. J., D. M. Gleeson, and M. N. Clout. "Measuring connectivity of invasive stoat populations to inform conservation management." Wildlife Research 41, no. 5 (2014): 395. http://dx.doi.org/10.1071/wr14015.
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Context Effective design of conservation management programs for long-term population control requires an accurate definition of the spatial extent of populations, along with a proper understanding of the ways that landscape patchiness influences demography and dispersal within these populations. Aims In the present study, genetic techniques are used to describe the population genetic structure and connectivity of invasive stoats (Mustela erminea) across the Auckland region, New Zealand, so as to assist planning for mainland stoat control, and define potential future eradication units. Methods A sample of stoats from across the region (n = 120), was genotyped at 17 microsatellite loci, and a combination of clustering, genetic population assignment and various migration estimation methods were applied to these data. Key results Moderate population structure was observed (FST = 0.03–0.21), with five geographic populations defined by genetic clustering. Almost all individuals were correctly assigned to the location of origin, and recent migration rates among forest patches were found to be low. Conclusions It is possible to define the origin of stoats at this regional scale using genetic measures. From this, we show that the stoat incursion on Rangitoto Island that occurred post-eradication in 2010 probably came from East Auckland (P < 0.0001), whereas the 2014 stoat incursion on Motutapu Island probably originated from a population linked to the Waitakeres. Also, the Waiheke Island stoat population has minimal connection to all other populations and it is therefore a potential eradication unit. Implications The low migration rates among forest patches indicated that if thorough control is imposed on a discrete forest patch, reinvasion from other forest patches will be relatively low. Importantly, for stoat control in the region, the isolation of the Waiheke Island stoat population means that eradication here is likely to be feasible with low reinvasion pressure.
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Krawiec, Josef, Siegfried L. Krauss, Robert A. Davis, and Peter B. S. Spencer. "Weak genetic structuring suggests historically high genetic connectivity among recently fragmented urban populations of the scincid lizard, Ctenotus fallens." Australian Journal of Zoology 63, no. 4 (2015): 279. http://dx.doi.org/10.1071/zo15022.
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Populations in fragmented urban remnants may be at risk of genetic erosion as a result of reduced gene flow and elevated levels of inbreeding. This may have serious genetic implications for the long-term viability of remnant populations, in addition to the more immediate pressures caused by urbanisation. The population genetic structure of the generalist skink Ctenotus fallens was examined using nine microsatellite markers within and among natural vegetation remnants within a highly fragmented urban matrix in the Perth metropolitan area in Western Australia. These data were compared with samples from a large unfragmented site on the edge of the urban area. Overall, estimates of genetic diversity and inbreeding within all populations were similar and low. Weak genetic differentiation, and a significant association between geographic and genetic distance, suggests historically strong genetic connectivity that decreases with geographic distance. Due to recent fragmentation, and genetic inertia associated with low genetic diversity and large population sizes, it is not possible from these data to infer current genetic connectivity levels. However, the historically high levels of gene flow that our data suggest indicate that a reduction in contemporary connectivity due to fragmentation in C. fallens is likely to result in negative genetic consequences in the longer term.
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Christie, Mark R., Patrick G. Meirmans, Oscar E. Gaggiotti, Robert J. Toonen, and Crow White. "Disentangling the relative merits and disadvantages of parentage analysis and assignment tests for inferring population connectivity." ICES Journal of Marine Science 74, no. 6 (April 7, 2017): 1749–62. http://dx.doi.org/10.1093/icesjms/fsx044.
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AbstractAccurately estimating patterns of population connectivity in marine systems remains an elusive goal. Current genetic approaches have focused on assigning individuals back to their natal populations using one of two methods: parentage analyses and assignment tests. Each of these approaches has their relative merits and weaknesses. Here, we illustrate these tradeoffs using a forward-time agent-based model that incorporates relevant natural history and physical oceanography for 135 Kellet’s whelk (Kelletia kelletii) populations from Southern California. Like most marine organisms, Kellet’s whelks live in large meta-populations where local populations are connected by dispersive larvae. For estimating population connectivity, we found parentage analyses to be relatively insensitive to the amount of genetic differentiation among local populations, but highly sensitive to the proportion of the meta-population sampled. Assignment tests, on the other hand, were relatively insensitive to the proportion of the meta-population sampled, but highly sensitive to the amount of genetic differentiation found among local populations. Comparisons between the true connectivity matrices (generated by using the true origin of all sampled individuals) and those obtained via parentage analyses and assignment tests reveal that neither approach can explain >26% of the variation in true connectivity. Furthermore, even with perfect assignment of all sampled individuals, sampling error alone can introduce noise into the estimated population connectivity matrix. Future work should aim to improve the number of correct assignments without the expense of additional incorrect assignments, perhaps by using dispersal information obtained from related individuals as priors in a Bayesian framework. These analyses dispel a number of common misconceptions in the field and highlight areas for both future research and methodological improvements.
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Serrano-Rodríguez, Anay, Griselda Escalona-Segura, Antonio González Rodríguez, Salima Machkour-M’Rabet, Lorena Ruiz-Montoya, Eduardo E. Iñigo Elias, and Alexis Herminio Plasencia-Vázquez. "Effects of Anthropogenic Habitat Fragmentation on the Genetic Connectivity of the Threatened and Endemic Campylorhynchus yucatanicus (Aves, Trogloditydae) in the Yucatan Peninsula, Mexico." Diversity 14, no. 12 (December 13, 2022): 1108. http://dx.doi.org/10.3390/d14121108.
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Identifying connectivity patterns among remnant bird populations and their relationships with land use practices and adjacent habitat fragments is key to implementing appropriate long-term management strategies for species conservation. The coastal scrub and dune vegetation complex of the northern Yucatan Peninsula is rich in endemisms and has been affected by human development, which threatens the survival of the Yucatan Wren (Campylorhynchus yucatanicus) population, an endemic bird species. To identify possible anthropogenic barriers to the connectivity of C. yucatanicus along 14 localities in the Yucatan (Mexico) coastal north, we explored the relationship between the species population’s genetic variability at each sampled site and landscape structure using regression models, in addition to the relationship between genetic distance and landscape resistance. Seven nuclear microsatellite loci were used as genetic markers. Four genetic populations were highlighted by the clustering method implemented in the Geneland program. Human settlement and availability of adequate habitat were significantly related to genetic distance (Fst), suggesting limited connectivity among sites due to ongoing land use changes. We suggest changing the IUCN threat category of C. yucatanicus to endangered as we found a significant loss of genetic variability in addition to restricted distribution, small population, habitat degradation, and loss of connectivity.
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Gauthier, Martha, Emily Crowe, Lindsey Hawke, Neil Emery, Paul Wilson, and Joanna Freeland. "Conservation genetics of Pitcher’s thistle (Cirsium pitcheri), an endangered Great Lakes endemic." Botany 88, no. 3 (March 2010): 250–57. http://dx.doi.org/10.1139/b10-006.
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Pitcher's thistle ( Cirsium pitcheri Torr. ex Eaton (Torr. & Gray)) is a Great Lakes endemic that in Canada is designated as threatened at both the provincial (Ontario) and national levels. Management plans will benefit from conservation genetic data, which can provide insight into population genetic diversity and differentiation. We obtained genetic data from nuclear and chloroplast microsatellite markers from 17 populations of C. pitcheri around the Great Lakes. The nuclear data revealed overall low levels of diversity, high levels of inbreeding, and low levels of population connectivity. The chloroplast data identified a single haplotype, which is consistent with reduced genetic diversity following postglacial colonization. The high levels of inbreeding within populations will likely pose a serious threat to populations in the short term; these have resulted from a combination of low connectivity between populations, and small and fluctuating population sizes. Future management of C. pitcheri populations should consider human-mediated dispersal of plants or seeds among sites.
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Ramírez, Oscar, Elena Gómez-Díaz, Iñigo Olalde, Juan Illera, Juan Rando, Jacob González-Solís, and Carles Lalueza-Fox. "Population connectivity buffers genetic diversity loss in a seabird." Frontiers in Zoology 10, no. 1 (2013): 28. http://dx.doi.org/10.1186/1742-9994-10-28.
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Chapuis, Marie-Pierre, Julie-Anne M. Popple, Karine Berthier, Stephen J. Simpson, Edward Deveson, Peter Spurgin, Martin J. Steinbauer, and Gregory A. Sword. "Challenges to assessing connectivity between massive populations of the Australian plague locust." Proceedings of the Royal Society B: Biological Sciences 278, no. 1721 (March 9, 2011): 3152–60. http://dx.doi.org/10.1098/rspb.2010.2605.
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Linking demographic and genetic dispersal measures is of fundamental importance for movement ecology and evolution. However, such integration can be difficult, particularly for highly fecund species that are often the target of management decisions guided by an understanding of population movement. Here, we present an example of how the influence of large population sizes can preclude genetic approaches from assessing demographic population structuring, even at a continental scale. The Australian plague locust, Chortoicetes terminifera , is a significant pest, with populations on the eastern and western sides of Australia having been monitored and managed independently to date. We used microsatellites to assess genetic variation in 12 C. terminifera population samples separated by up to 3000 km. Traditional summary statistics indicated high levels of genetic diversity and a surprising lack of population structure across the entire range. An approximate Bayesian computation treatment indicated that levels of genetic diversity in C. terminifera corresponded to effective population sizes conservatively composed of tens of thousands to several million individuals. We used these estimates and computer simulations to estimate the minimum rate of dispersal, m , that could account for the observed range-wide genetic homogeneity. The rate of dispersal between both sides of the Australian continent could be several orders of magnitude lower than that typically considered as required for the demographic connectivity of populations.
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Jaun, Andreas, Hans-Peter Wymann, and Kay Lucek. "Lack of genetic structure suggests high connectivity of Parnassius phoebus between nearby valleys in the Alps." Alpine Entomology 6 (March 24, 2022): 1–6. http://dx.doi.org/10.3897/alpento.6.80405.
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The spatial scale of intraspecific genetic connectivity and population structure are important aspects of conservation genetics. However, for many species these properties are unknown. Here we used genomic data to assess the genetic structure of the small Apollo butterfly (Parnassius phoebus Fabricius, 1793; Lepidoptera: Papilionidae) across three nearby valleys in the Central Swiss Alps. One of the valleys is currently used for hydropower production with future plans to raise the existing dam wall further. We found no significant genetic structure, suggesting a currently high connectivity of this species in our studied region.
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LaCava, Melanie E. F., Roderick B. Gagne, Sierra M. Love Stowell, Kyle D. Gustafson, C. Alex Buerkle, Lee Knox, and Holly B. Ernest. "Pronghorn population genomics show connectivity in the core of their range." Journal of Mammalogy 101, no. 4 (May 29, 2020): 1061–71. http://dx.doi.org/10.1093/jmammal/gyaa054.
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Abstract Preserving connectivity in the core of a species’ range is crucial for long-term persistence. However, a combination of ecological characteristics, social behavior, and landscape features can reduce connectivity among wildlife populations and lead to genetic structure. Pronghorn (Antilocapra americana), for example, exhibit fluctuating herd dynamics and variable seasonal migration strategies, but GPS tracking studies show that landscape features such as highways impede their movements, leading to conflicting hypotheses about expected levels of genetic structure. Given that pronghorn populations declined significantly in the early 1900s, have only partially recovered, and are experiencing modern threats from landscape modification, conserving connectivity among populations is important for their long-term persistence in North America. To assess the genetic structure and diversity of pronghorn in the core of their range, we genotyped 4,949 genome-wide single-nucleotide polymorphisms and 11 microsatellites from 398 individuals throughout the state of Wyoming. We found no evidence of genetic subdivision and minimal evidence of isolation by distance despite a range that spans hundreds of kilometers, multiple mountain ranges, and three interstate highways. In addition, a rare variant analysis using putatively recent mutations found no genetic division between pronghorn on either side of a major highway corridor. Although we found no evidence that barriers to daily and seasonal movements of pronghorn impede gene flow, we suggest periodic monitoring of genetic structure and diversity as a part of management strategies to identify changes in connectivity.
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Rodger, Yael S., Alexandra Pavlova, Steve Sinclair, Melinda Pickup, and Paul Sunnucks. "Evolutionary history and genetic connectivity across highly fragmented populations of an endangered daisy." Heredity 126, no. 5 (February 19, 2021): 846–58. http://dx.doi.org/10.1038/s41437-021-00413-0.
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AbstractConservation management can be aided by knowledge of genetic diversity and evolutionary history, so that ecological and evolutionary processes can be preserved. The Button Wrinklewort daisy (Rutidosis leptorrhynchoides) was a common component of grassy ecosystems in south-eastern Australia. It is now endangered due to extensive habitat loss and the impacts of livestock grazing, and is currently restricted to a few small populations in two regions >500 km apart, one in Victoria, the other in the Australian Capital Territory and nearby New South Wales (ACT/NSW). Using a genome-wide SNP dataset, we assessed patterns of genetic structure and genetic differentiation of 12 natural diploid populations. We estimated intrapopulation genetic diversity to scope sources for genetic management. Bayesian clustering and principal coordinate analyses showed strong population genetic differentiation between the two regions, and substantial substructure within ACT/NSW. A coalescent tree-building approach implemented in SNAPP indicated evolutionary divergence between the two distant regions. Among the populations screened, the last two known remaining Victorian populations had the highest genetic diversity, despite having among the lowest recent census sizes. A maximum likelihood population tree method implemented in TreeMix suggested little or no recent gene flow except potentially between very close neighbours. Populations that were more genetically distinctive had lower genetic diversity, suggesting that drift in isolation is likely driving population differentiation though loss of diversity, hence re-establishing gene flow among them is desirable. These results provide background knowledge for evidence-based conservation and support genetic rescue within and between regions to elevate genetic diversity and alleviate inbreeding.
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Gerlach, Gabriele, Philipp Kraemer, Peggy Weist, Laura Eickelmann, and Michael J. Kingsford. "Impact of cyclones on hard coral and metapopulation structure, connectivity and genetic diversity of coral reef fish." Coral Reefs 40, no. 4 (May 18, 2021): 999–1011. http://dx.doi.org/10.1007/s00338-021-02096-9.
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AbstractCyclones have one of the greatest effects on the biodiversity of coral reefs and the associated species. But it is unknown how stochastic alterations in habitat structure influence metapopulation structure, connectivity and genetic diversity. From 1993 to 2018, the reefs of the Capricorn Bunker Reef group in the southern part of the Great Barrier Reef were impacted by three tropical cyclones including cyclone Hamish (2009, category 5). This resulted in substantial loss of live habitat-forming coral and coral reef fish communities. Within 6–8 years after cyclones had devastated, live hard corals recovered by 50–60%. We show the relationship between hard coral cover and the abundance of the neon damselfish (Pomacentrus coelestis), the first fish colonizing destroyed reefs. We present the first long-term (2008–2015 years corresponding to 16–24 generations of P. coelestis) population genetic study to understand the impact of cyclones on the meta-population structure, connectivity and genetic diversity of the neon damselfish. After the cyclone, we observed the largest change in the genetic structure at reef populations compared to other years. Simultaneously, allelic richness of genetic microsatellite markers dropped indicating a great loss of genetic diversity, which increased again in subsequent years. Over years, metapopulation dynamics were characterized by high connectivity among fish populations associated with the Capricorn Bunker reefs (2200 km2); however, despite high exchange, genetic patchiness was observed with annual strong genetic divergence between populations among reefs. Some broad similarities in the genetic structure in 2015 could be explained by dispersal from a source reef and the related expansion of local populations. This study has shown that alternating cyclone-driven changes and subsequent recovery phases of coral habitat can greatly influence patterns of reef fish connectivity. The frequency of disturbances determines abundance of fish and genetic diversity within species.
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Tang, Lei Stanley, Carolyn Smith-Keune, Anthony C. Grice, James M. Moloney, and Britta Denise Hardesty. "Genetic structure and diversity of the black-throated finch (Poephila cincta) across its current range." Australian Journal of Zoology 64, no. 6 (2016): 375. http://dx.doi.org/10.1071/zo16073.
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Understanding the patterns of population connectivity and level of genetic diversity can facilitate the identification of both ecologically relevant populations and the spatial scales at which conservation management may need to focus. We quantified genetic variation within and among populations of black-throated finches across their current distribution. To quantify genetic structure and diversity, we genotyped 242 individuals from four populations using 14 polymorphic microsatellite markers and sequenced 25 individuals based on a 302-base-pair segment of mitochondrial control region. We found modest levels of genetic diversity (average allelic richness r = 4.37 ± 0.41 (standard error) and average heterozygosity HO = 0.42 ± 0.040 (standard error)) with no bottleneck signature among sampled populations. We identified two genetic groups that represent populations of two subspecies based on Bayesian clustering analysis and low levels of genetic differentiation based on pairwise genetic differentiation statistics (all FST, RST and Nei’s unbiased D values <0.1). Our data suggest that genetic exchange occurs among sampled populations despite recent population declines. Conservation efforts that focus on maintaining habitat connectivity and increasing habitat quality to ensure a high level of gene flow on a larger scale will improve the species’ ability to persist in changing landscapes. Conservation management should also support continuous monitoring of the bird to identify any rapid population declines as land-use intensification occurs throughout the species’ range.
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Ovenden, Jennifer R. "Crinkles in connectivity: combining genetics and other types of biological data to estimate movement and interbreeding between populations." Marine and Freshwater Research 64, no. 3 (2013): 201. http://dx.doi.org/10.1071/mf12314.
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Marine species generally have large population sizes, continuous distributions and high dispersal capacity. Despite this, they are often subdivided into separate populations, which are the basic units of fisheries management. For example, populations of some fisheries species across the deep water of the Timor Trench are genetically different, inferring minimal movement and interbreeding. When connectivity is higher than the Timor Trench example, but not so high that the populations become one, connectivity between populations is crinkled. Crinkled connectivity occurs when migration is above the threshold required to link populations genetically, but below the threshold for demographic links. In future, genetic estimates of connectivity over crinkled links could be uniquely combined with other data, such as estimates of population size and tagging and tracking data, to quantify demographic connectedness between these types of populations. Elasmobranch species may be ideal targets for this research because connectivity between populations is more likely to be crinkled than for finfish species. Fisheries stock-assessment models could be strengthened with estimates of connectivity to improve the strategic and sustainable harvesting of biological resources.
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Skroblin, Anja, Andrew Cockburn, and Sarah Legge. "The population genetics of the western purple-crowned fairy-wren (Malurus coronatus coronatus), a declining riparian passerine." Australian Journal of Zoology 62, no. 3 (2014): 251. http://dx.doi.org/10.1071/zo13087.
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We investigate the population genetic structure of the declining western subspecies of the purple-crowned fairy-wren (Malurus coronatus coronatus) in order to guide conservation management recommendations for this riparian habitat specialist. Our analysis of multilocus microsatellite data, from 79 individuals sampled from across the species’ range, indicates that M. c. coronatus occurs as genetically differentiated subpopulations that correspond to catchment boundaries or expansive gaps in habitat along waterways. The genetic similarity of large populations of fairy-wrens on four catchments (Fitzroy, Durack, Drysdale and Victoria) indicates widespread recent gene flow, whereas the high genetic distinctiveness of the Bindoola and Isdell catchments may reflect the current geographic isolation of these smaller populations. Genetic differentiation of these smaller geographically isolated populations affirms the negative effect that habitat degradation and fragmentation can have on population connectivity. A regional-scale approach to conservation with a focus on preventing degradation and enhancing connectivity may be critical to safeguard the persistence of M. c. coronatus subpopulations.
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Smith, Timothy M., Corey P. Green, and Craig D. H. Sherman. "Patterns of connectivity and population structure of the southern calamary Sepioteuthis australis in southern Australia." Marine and Freshwater Research 66, no. 10 (2015): 942. http://dx.doi.org/10.1071/mf14328.
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The southern calamary, Sepioteuthis australis, is a commercially and recreationally important inshore cephalopod endemic to southern Australia and New Zealand. Typical of other cephalopods, S. australis has a short life span, form nearshore spawning aggregations and undergo direct development. Such life history traits may restrict connectivity between spawning grounds creating highly structured and genetically differentiated populations that are susceptible to population crashes. Here we use seven polymorphic microsatellite markers to assess connectivity and population structure of S. australis across a large part of its geographic range in Australia. Little genetic differentiation was found between sampling locations. Overall, FST was low (0.005, 95% CI=<0.001–0.011) and we detected no significant genetic differentiation between any of the locations sampled. There was no strong relationship between genetic and geographical distance, and our neighbour joining analysis did not show clustering of clades based on geographical locations. Similarly, network analysis showed strong connectivity amongst most locations, in particular, Tasmania appears to be well connected with several other locations and may act as an important source population. High levels of gene flow and connectivity between S. australis sampling sites across Australia are important for this short-lived species, ensuring resilience against spatial and temporal mortality fluctuations.
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Silva, C. N. S., H. S. Macdonald, M. G. Hadfield, M. Cryer, and J. P. A. Gardner. "Ocean currents predict fine-scale genetic structure and source-sink dynamics in a marine invertebrate coastal fishery." ICES Journal of Marine Science 76, no. 4 (January 28, 2019): 1007–18. http://dx.doi.org/10.1093/icesjms/fsy201.
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Abstract Estimates of connectivity are vital for understanding population dynamics and for the design of spatial management areas. However, this is still a major challenge in the marine environment because the relative contributions of factors influencing connectivity amongst subpopulations are difficult to assess. This study combined population genetics with hydrodynamic modelling (Regional Ocean Modeling System, ROMS) to assess spatial and temporal exchange of individuals among subpopulations of the New Zealand scallop, Pecten novaezelandiae, within the Coromandel fishery area open to commercial fishing. Significant genetic differentiation was revealed among subpopulations with variable levels of recruitment. Connectivity, as assessed by ROMS, was a significant explanatory variable of genetic differentiation when accounting for the spatial dependency between locations. Although additional research is needed before source-sink population dynamics can be confidently used in management, these results imply that higher yields could be available from this fishery at lower risk of over-exploitation if the fishing of each subpopulation could be tailored to its contribution to recruitment, perhaps using subpopulation catch limits. This study highlights inter-annual patterns of connectivity, the importance of combining different methods for a better prediction of population dynamics, and how such an approach may contribute to management of living marine resources.
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Salas, E. M., G. Bernardi, M. L. Berumen, M. R. Gaither, and L. A. Rocha. "RADseq analyses reveal concordant Indian Ocean biogeographic and phylogeographic boundaries in the reef fish Dascyllus trimaculatus." Royal Society Open Science 6, no. 5 (May 2019): 172413. http://dx.doi.org/10.1098/rsos.172413.
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Population genetic analysis is an important tool for estimating the degree of evolutionary connectivity in marine organisms. Here, we investigate the population structure of the three-spot damselfish Dascyllus trimaculatus in the Red Sea, Arabian Sea and Western Indian Ocean, using 1174 single nucleotide polymorphisms (SNPs). Neutral loci revealed a signature of weak genetic differentiation between the Northwestern (Red Sea and Arabian Sea) and Western Indian Ocean biogeographic provinces. Loci potentially under selection (outlier loci) revealed a similar pattern but with a much stronger signal of genetic structure between regions. The Oman population appears to be genetically distinct from all other populations included in the analysis. While we could not clearly identify the mechanisms driving these patterns (isolation, adaptation or both), the datasets indicate that population-level divergences are largely concordant with biogeographic boundaries based on species composition. Our data can be used along with genetic connectivity of other species to identify the common genetic breaks that need to be considered for the conservation of biodiversity and evolutionary processes in the poorly studied Western Indian Ocean region.
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Anthonysamy, Whitney J. B., Michael J. Dreslik, Sarah J. Baker, Mark A. Davis, Marlis R. Douglas, Michael E. Douglas, and Christopher A. Phillips. "Limited gene flow and pronounced population genetic structure of Eastern Massasauga (Sistrurus catenatus) in a Midwestern prairie remnant." PLOS ONE 17, no. 3 (March 24, 2022): e0265666. http://dx.doi.org/10.1371/journal.pone.0265666.
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As anthropogenic changes continue to ecologically stress wildlife, obtaining measures of gene flow and genetic diversity are crucial for evaluating population trends and considering management and conservation strategies for small, imperiled populations. In our study, we conducted a molecular assessment to expand on previous work to elucidate patterns of diversity and connectivity in the remaining disjunct Eastern Massasauga Rattlesnake (Sistrurus catenatus) hibernacula in Illinois. We assayed genetic data for 327 samples collected during 1999–2015 from the Carlyle Lake study area across 21 microsatellite loci. We found hibernacula formed distinct genetic clusters corresponding to the three main study areas (Dam Recreation Areas, Eldon Hazlet State Park, and South Shore State Park). Genetic structuring and low estimates of dispersal indicated that connectivity among these study areas is limited and each is demographically independent. Hibernacula exhibited moderate levels of heterozygosity (0.60–0.73), but estimates of effective population size (5.2–41.0) were low and track census sizes generated via long-term mark-recapture data. Hibernacula at Carlyle Lake, which represent the only Eastern Massasauga remaining in Illinois, are vulnerable to future loss of genetic diversity through lack of gene flow as well as demographic and environmental stochastic processes. Our work highlights the need to include population-level genetic data in recovery planning and suggests that recovery efforts should focus on managing the three major study areas as separate conservation units in order to preserve and maintain long-term adaptive potential of these populations. Specific management goals should include improving connectivity among hibernacula, maintaining existing wet grassland habitat, and minimizing anthropogenic sources of mortality caused by habitat management (e.g., mowing, prescribed fire) and recreational activities. Our molecular study provides additional details about demographic parameters and connectivity at Carlyle Lake that can be used to guide recovery of Eastern Massasauga in Illinois and throughout its range.
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Chaiyes, Aingorn, Nattakan Ariyaraphong, Ngamphrom Sukgosa, Kornsuang Jangtarwan, Syed Farhan Ahmad, Nararat Laopichienpong, Worapong Singchat, et al. "Evidence of Genetic Connectivity among Lyle’s Flying Fox Populations in Thailand for Wildlife Management and One Health Framework." Sustainability 14, no. 17 (August 30, 2022): 10791. http://dx.doi.org/10.3390/su141710791.
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Bats are important reservoir hosts of emerging viruses. Recent viral outbreaks and pandemics have resulted in an increased research focus on the genetic diversity, population structure, and distribution of bat species. Lyle’s flying fox (Pteropus lylei) is widely distributed throughout central Thailand, with most colonies congregating in temples within proximity to humans. A lack of knowledge regarding the genetic connectivity among different colonies hinders the investigation of zoonotic disease epidemiology and wildlife management. In this study, we hypothesized that genetic material may be exchanged between Lyle’s flying fox colonies that live in proximity. We assessed the mitochondrial displacement loop and cytochrome b nucleotide sequences of samples collected from 94 individuals from ten colonies across different roosting sites and detected limited genetic differentiation but increased nucleotide divergence within colonies. This suggests that genetic connectivity among Lyle’s flying fox colonies has experienced frequent and recent gene flow. These findings indicate that this species has maintained demographic equilibrium in a stable population, with a slight expansion event in certain populations. These data provide insights into the dynamics of bat populations, and the genetic knowledge gained presents opportunities for the improved monitoring of bat population structure.
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Skroblin, Anja, Robert Lanfear, Andrew Cockburn, and Sarah Legge. "Inferring population connectivity across the range of the purple-crowned fairy-wren (Malurus coronatus) from mitochondrial DNA and morphology: implications for conservation management." Australian Journal of Zoology 60, no. 3 (2012): 199. http://dx.doi.org/10.1071/zo12093.
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Knowledge of population structure and patterns of connectivity is required to implement effective conservation measures for the purple-crowned fairy-wren (Malurus coronatus), a threatened endemic of northern Australia. This study aimed to identify barriers to dispersal across the distribution of M. coronatus, investigate the impact that the recent declines may have on population connectivity, and propose conservation actions to maintain natural patterns of gene flow. Analysis of mitochondrial DNA sequences from 87 M. coronatus identified two phylogenetic clusters that corresponded with the phenotypically defined western (M. c. coronatus) and eastern (M. c. macgillivrayi) subspecies. The genetic divergence between these subspecies was consistent with isolation by a natural barrier to gene flow, and supports their separate conservation management. Within the declining M. c. coronatus, the lack of genetic divergence and only slight morphological difference between remnant populations indicates that populations were recently linked by gene flow. It is likely that widespread habitat degradation and the recent extirpation of M. c. coronatus from the Ord River will disrupt connectivity between, and dynamics within, remnant populations. To prevent further declines, conservation of M. coronatus must preserve areas of quality habitat and restore connectivity between isolated populations.
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Tay, Y. C., M. W. P. Chng, W. W. G. Sew, F. E. Rheindt, K. P. P. Tun, and R. Meier. "Beyond the Coral Triangle: high genetic diversity and near panmixia in Singapore's populations of the broadcast spawning sea star Protoreaster nodosus." Royal Society Open Science 3, no. 8 (August 2016): 160253. http://dx.doi.org/10.1098/rsos.160253.
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The Coral Triangle is widely considered the most important centre of marine biodiversity in Asia while areas on its periphery such as the South China Sea, have received much less interest. Here, we demonstrate that a small population of the knobbly sea star Protoreaster nodosus in Singapore has similarly high levels of genetic diversity as comparable Indonesian populations from the Coral Triangle. The high genetic diversity of this population is remarkable because it is maintained despite decades of continued anthropogenic disturbance. We postulate that it is probably due to broadcast spawning which is likely to maintain high levels of population connectivity. To test this, we analysed 6140 genome-wide single nucleotide polymorphism (SNP) loci for Singapore's populations and demonstrate a pattern of near panmixia. We here document a second case of high genetic diversity and low genetic structure for a broadcast spawner in Singapore, which suggests that such species have high resilience against anthropogenic disturbances. The study demonstrates the feasibility and power of using genome-wide SNPs for connectivity studies of marine invertebrates without a sequenced genome.
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Liu, Shang Yin Vanson, Shoou Jeng Joung, Chi-Ju Yu, Hua-Hsun Hsu, Wen-Pei Tsai, and Kwang Ming Liu. "Genetic diversity and connectivity of the megamouth shark (Megachasma pelagios)." PeerJ 6 (March 5, 2018): e4432. http://dx.doi.org/10.7717/peerj.4432.
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The megamouth shark (Megachasma pelagios) was described as a new species in 1983. Since then, only ca. 100 individuals have been observed or caught. Its horizontal migration, dispersal, and connectivity patterns are still unknown due to its rarity. Two genetic markers were used in this study to reveal its genetic diversity and connectivity pattern. This approach provides a proxy to indirectly measure gene flow between populations. Tissues from 27 megamouth sharks caught by drift nets off the Hualien coast (eastern Taiwan) were collected from 2013 to 2015. With two additional tissue samples from megamouths caught in Baja California, Mexico, and sequences obtained from GenBank, we were able to perform the first population genetic analyses of the megamouth shark. The mtDNA cox1 gene and a microsatellite (Loc 6) were sequenced and analyzed. Our results showed that there is no genetic structure in the megamouth shark, suggesting a possible panmictic population. Based on occurrence data, we also suggest that the Kuroshio region, including the Philippines, Taiwan, and Japan, may act as a passageway for megamouth sharks to reach their feeding grounds from April to August. Our results provide insights into the dispersal and connectivity of megamouth sharks. Future studies should focus on collecting more samples and conducting satellite tagging to better understand the global migration and connectivity pattern of the megamouth shark.
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Baltazar-Soares, Miguel, Hans-Harald Hinrichsen, and Christophe Eizaguirre. "Integrating population genomics and biophysical models towards evolutionary-based fisheries management." ICES Journal of Marine Science 75, no. 4 (January 6, 2018): 1245–57. http://dx.doi.org/10.1093/icesjms/fsx244.
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Abstract Overfishing and rapid environmental shifts pose severe challenges to the resilience and viability of marine fish populations. To develop and implement measures that enhance species’ adaptive potential to cope with those pressures while, at the same time, ensuring sustainable exploitation rates is part of the central goal of fisheries management. Here, we argue that a combination of biophysical modelling and population genomic assessments offer ideal management tools to define stocks, their physical connectivity and ultimately, their short-term adaptive potential. To date, biophysical modelling has often been confined to fisheries ecology whereas evolutionary hypotheses remain rarely considered. When identified, connectivity patterns are seldom explored to understand the evolution and distribution of adaptive genetic variation, a proxy for species’ evolutionary potential. Here, we describe a framework that expands on the conventional seascape genetics approach by using biophysical modelling and population genomics. The goals are to identify connectivity patterns and selective pressures, as well as putative adaptive variants directly responding to the selective pressures and, ultimately, link both to define testable hypotheses over species response to shifting ecological conditions and overexploitation.
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Casabianca, Silvia, Antonella Penna, Elena Pecchioli, Antoni Jordi, Gotzon Basterretxea, and Cristiano Vernesi. "Population genetic structure and connectivity of the harmful dinoflagellate Alexandrium minutum in the Mediterranean Sea." Proceedings of the Royal Society B: Biological Sciences 279, no. 1726 (May 18, 2011): 129–38. http://dx.doi.org/10.1098/rspb.2011.0708.
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The toxin-producing microbial species Alexandrium minutum has a wide distribution in the Mediterranean Sea and causes high biomass blooms with consequences on the environment, human health and coastal-related economic activities. Comprehension of algal genetic differences and associated connectivity is fundamental to understand the geographical scale of adaptation and dispersal pathways of harmful microalgal species. In the present study, we combine A. minutum population genetic analyses based on microsatellites with indirect connectivity ( C i ) estimations derived from a general circulation model of the Mediterranean sea. Our results show that four major clusters of genetically homogeneous groups can be identified, loosely corresponding to four regional seas: Adriatic, Ionian, Tyrrhenian and Catalan. Each of the four clusters included a small fraction of mixed and allochthonous genotypes from other Mediterranean areas, but the assignment to one of the four clusters was sufficiently robust as proved by the high ancestry coefficient values displayed by most of the individuals (>84%). The population structure of A. minutum on this scale can be explained by microalgal dispersion following the main regional circulation patterns over successive generations. We hypothesize that limited connectivity among the A. minutum populations results in low gene flow but not in the erosion of variability within the population, as indicated by the high gene diversity values. This study represents a first and new integrated approach, combining both genetic and numerical methods, to characterize and interpret the population structure of a toxic microalgal species. This approach of characterizing genetic population structure and connectivity at a regional scale holds promise for the control and management of the harmful algal bloom events in the Mediterranean Sea.
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Jenkins, Deborah A., Nicolas Lecomte, James A. Schaefer, Steffen M. Olsen, Didier Swingedouw, Steeve D. Côté, Loïc Pellissier, and Glenn Yannic. "Loss of connectivity among island-dwelling Peary caribou following sea ice decline." Biology Letters 12, no. 9 (September 2016): 20160235. http://dx.doi.org/10.1098/rsbl.2016.0235.
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Global warming threatens to reduce population connectivity for terrestrial wildlife through significant and rapid changes to sea ice. Using genetic fingerprinting, we contrasted extant connectivity in island-dwelling Peary caribou in northern Canada with continental-migratory caribou. We next examined if sea-ice contractions in the last decades modulated population connectivity and explored the possible impact of future climate change on long-term connectivity among island caribou. We found a strong correlation between genetic and geodesic distances for both continental and Peary caribou, even after accounting for the possible effect of sea surface. Sea ice has thus been an effective corridor for Peary caribou, promoting inter-island connectivity and population mixing. Using a time series of remote sensing sea-ice data, we show that landscape resistance in the Canadian Arctic Archipelago has increased by approximately 15% since 1979 and may further increase by 20–77% by 2086 under a high-emission scenario (RCP8.5). Under the persistent increase in greenhouse gas concentrations, reduced connectivity may isolate island-dwelling caribou with potentially significant consequences for population viability.
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Liu, Shang-Yin Vanson, Chia-Hui Wang, Jen-Chieh Shiao, and Chang-Feng Dai. "Population connectivity of neon damsel, Pomacentrus coelestis, inferred from otolith microchemistry and mtDNA." Marine and Freshwater Research 61, no. 12 (2010): 1416. http://dx.doi.org/10.1071/mf10079.
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Understanding dispersal patterns and population connectivity is crucial to the conservation and management of fish assemblages in reef ecosystems. To reveal the population connectivity of reef fishes in the northern West Pacific, we examined the otolith chemistry and the mtDNA control region of Pomacentrus coelestis collected from six localities between Hainan Island (China) and Okinawa (Japan). The results of otolith chemistry analyses on pre-settlement signatures showed that fishes in north-west Taiwan may have a similar origin, whereas those in southern Taiwan might have a separate origin from the South China Sea. Furthermore, the elemental ratios of post-settlement signatures showed clear separation among localities, reflecting their sedentary behaviour after settlement and the influence of local environment. Population genetic analyses revealed that significant genetic differentiation occurred between populations in north-west Taiwan and populations in the South China Sea and the Kuroshio ecosystems. This study demonstrated that otolith chemistry and mtDNA analyses revealed consistent and complementary results of the dispersal and connectivity of P. coelestis populations, and provided evidence supporting that fish populations around Taiwan should be considered as two stocks. Thus, two marine protected area networks should be established for the conservation and management of reef fishes in this area.
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Dodge, DL, MS Studivan, RJ Eckert, E. Chei, J. Beal, and JD Voss. "Population structure of the scleractinian coral Montastraea cavernosa in southeast Florida." Bulletin of Marine Science 96, no. 4 (October 1, 2020): 767–82. http://dx.doi.org/10.5343/bms.2019.0074.
Full textAbstract:
The persistence of scleractinian coral populations on the Florida Reef Tract (FRT) is controlled in part by metapopulation dynamics and larval dispersal. Nine polymorphic microsatellite loci were analyzed to characterize contemporary population structure and gene flow as well as historical migration rates of Montastraea cavernosa at five sites off Martin, Palm Beach, and Broward counties in southeast Florida. The sampled populations demonstrated evidence of genetic isolation by distance over a geographic range of 85 km. Population genetic structure was divided into two genetic clusters, northern and southern, with admixture along a latitudinal gradient. Historical migration models indicated likely panmixia throughout all sites sampled, identifying a potential reduction in connectivity among the sampled populations through time. Though M. cavernosa populations demonstrated evidence of historical connectivity, contemporary patterns of isolation by distance suggest that effective management will require localized actions to maximize the likelihood of sustaining individual populations in the northern FRT. Given the results of this study, coupled with recent coral mortality events in the region, we recommend regional conservation efforts and management initiatives throughout southeast Florida within a more comprehensive FRT-wide management network.
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Ovenden, Jennifer R., Bree J. Tillett, Michael Macbeth, Damien Broderick, Fiona Filardo, Raewyn Street, Sean R. Tracey, and Jayson Semmens. "Stirred but not shaken: population and recruitment genetics of the scallop (Pecten fumatus) in Bass Strait, Australia." ICES Journal of Marine Science 73, no. 9 (May 8, 2016): 2333–41. http://dx.doi.org/10.1093/icesjms/fsw068.
Full textAbstract:
Abstract We report population genetic structure and fine-scale recruitment processes for the scallop beds (Pecten fumatus) in Bass Strait and the eastern coastline of Tasmania in southern Australia. Conventional population pairwise FST analyses are compared with novel discriminant analysis of principal components (DAPC) to assess population genetic structure using allelic variation in 11 microsatellite loci. Fine-scale population connectivity was compared with oceanic features of the sampled area. Disjunct scallop beds were genetically distinct, but there was little population genetic structure between beds connected by tides and oceanic currents. To identify recruitment patterns among and within beds, pedigree analyses determined the distribution of parent–offspring and sibling relationships in the sampled populations. Beds in northeastern Bass Strait were genetically distinct to adjacent beds (FST 0.003–0.005) and may not contribute to wider recruitment based on biophysical models of larval movement. Unfortunately, pedigree analyses lacked power to further dissect fine-scale recruitment processes including self-recruitment. Our results support the management of disjunct populations as separate stocks and the protection of source populations among open water beds. The application of DAPC and parentage analyses in the current study provided valuable insight into their potential power to determine population connectivity in marine species with larval dispersal.
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López, Benjamín, Omar Mejía, and Gerardo Zúñiga. "The effect of landscape on functional connectivity and shell shape in the land snail Humboldtiana durangoensis." PeerJ 8 (May 20, 2020): e9177. http://dx.doi.org/10.7717/peerj.9177.
Full textAbstract:
The populations of Humboldtiana durangoensis have experienced a drastic reduction in the effective population size; in addition, the species is threatened by anthropogenic activities. For the aforementioned, landscape genetics will serve as a tool to define the potential evolutionarily significant units (ESU) for this species. To complete our objective, we evaluated the effect of cover vegetation and climate on the functional connectivity of the species from the last glacial maximum (LGM) to the present as well as the effect of climate on shell shape. Partial Mantel tests, distance-based redundance analysis and a Bayesian framework were used to evaluate connectivity. On the other hand, geometric morphometrics, phylogenetic principal component analysis and redundancy analysis were used for the analysis of shell shape. Our results suggest that the suitable areas have been decreasing since the LGM; also, vegetation cover rather than climate has influenced the genetic connectivity among land snail populations, although temperature had a high influence on shell shape in this species. In conclusion, vegetation cover was the main factor that determined the functional connectivity for the land snail; however, local selective pressures led to different phenotypes in shell shape that allowed us to postulate that each one of the previously defined genetic groups must be considered as a different ESU.
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Shaddick, Kim, Dean M. Gilligan, Christopher P. Burridge, Dean R. Jerry, Kiet Truong, and Luciano B. Beheregaray. "Historic divergence with contemporary connectivity in a catadromous fish, the estuary perch (Macquaria colonorum)." Canadian Journal of Fisheries and Aquatic Sciences 68, no. 2 (February 2011): 304–18. http://dx.doi.org/10.1139/f10-139.
Full textAbstract:
The estuary perch ( Macquaria colonorum ) represents an important model for assessing how historical changes in coastal geomorphology and current oceanographic and estuarine conditions may have impacted connectivity in a catadromous fish. A fragment of the mitochondrial control region and six microsatellite DNA markers were used to clarify connectivity in 17 populations (n = 354) of estuary perch from the southeast and southern coasts of Australia. The mtDNA data showed a latitudinal disjunction in haplotype frequencies that divided populations into two groups (ΦST = 0.419), in a pattern suggestive of isolation by geographic distance. However, no marked structure or correlation with distance was apparent within each group, a result consistent with microsatellite data that showed high contemporary population connectivity across large distances. This was contrary to expectations that the species would exhibit moderate to strong genetic structure consistent with a one-dimensional stepping stone pattern. Coalescent phylogeographic and population genetic analyses provided support for a historical divergence probably due to the emergence of the Bassian Isthmus in southern Australia. Current connectivity appears to be maintained by both large- and fine-scale oceanographic currents and processes, highlighting the important role of the marine environment for an estuarine resident species.
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Ishiyama, N., M. Sueyoshi, and F. Nakamura. "To what extent do human-altered landscapes retain population connectivity? Historical changes in gene flow of wetland fish Pungitius pungitius." Royal Society Open Science 2, no. 7 (July 2015): 150033. http://dx.doi.org/10.1098/rsos.150033.
Full textAbstract:
Understanding how human-altered landscapes affect population connectivity is valuable for conservation planning. Natural connectivity among wetlands, which is maintained by floods, is disappearing owing to farmland expansion. Using genetic data, we assessed historical changes in the population connectivity of the ninespine stickleback within a human-altered wetland system. We predicted that: (i) the contemporary gene flow maintained by the artificial watercourse network may be restricted to a smaller spatial scale compared with the gene flow preceding alteration, and (ii) the contemporary gene flow is dominated by the downstream direction owing to the construction of low-head barriers. We evaluated the potential source population in both timescales. Seventeen studied populations were grouped into four genetically different clusters, and we estimated the migration rates among these clusters. Contemporary migration was restricted to between neighbouring clusters, although a directional change was not detected. Furthermore, we consistently found the same potential source cluster, from past to present, characterized by large amounts of remnant habitats connected by artificial watercourses. These findings highlight that: (i) artificial connectivity can sustain the short-distance connectivity of the ninespine stickleback, which contributes to maintaining the potential source populations; however, (ii) population connectivity throughout the landscape has been prevented by agricultural developments.
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Spies, Ingrid, Lorenz Hauser, Per Erik Jorde, Halvor Knutsen, André E. Punt, Lauren A. Rogers, and Nils Chr Stenseth. "Inferring genetic connectivity in real populations, exemplified by coastal and oceanic Atlantic cod." Proceedings of the National Academy of Sciences 115, no. 19 (April 19, 2018): 4945–50. http://dx.doi.org/10.1073/pnas.1800096115.
Full textAbstract:
Genetic data are commonly used to estimate connectivity between putative populations, but translating them to demographic dispersal rates is complicated. Theoretical equations that infer a migration rate based on the genetic estimator FST, such as Wright’s equation, FST ≈ 1/(4Nem + 1), make assumptions that do not apply to most real populations. How complexities inherent to real populations affect migration was exemplified by Atlantic cod in the North Sea and Skagerrak and was examined within an age-structured model that incorporated genetic markers. Migration was determined under various scenarios by varying the number of simulated migrants until the mean simulated level of genetic differentiation matched a fixed level of genetic differentiation equal to empirical estimates. Parameters that decreased the Ne/Nt ratio (where Ne is the effective and Nt is the total population size), such as high fishing mortality and high fishing gear selectivity, increased the number of migrants required to achieve empirical levels of genetic differentiation. Higher maturity-at-age and lower selectivity increased Ne/Nt and decreased migration when genetic differentiation was fixed. Changes in natural mortality, fishing gear selectivity, and maturity-at-age within expected limits had a moderate effect on migration when genetic differentiation was held constant. Changes in population size had the greatest effect on the number of migrants to achieve fixed levels of FST, particularly when genetic differentiation was low, FST ≈ 10−3. Highly variable migration patterns, compared with constant migration, resulted in higher variance in genetic differentiation and higher extreme values. Results are compared with and provide insight into the use of theoretical equations to estimate migration among real populations.
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Exadactylos, Athanasios, Dimitrios Vafidis, Costas Tsigenopoulos, and Georgios Gkafas. "High Connectivity of the White Seabream (Diplodus sargus, L. 1758) in the Aegean Sea, Eastern Mediterranean Basin." Animals 9, no. 11 (November 15, 2019): 979. http://dx.doi.org/10.3390/ani9110979.
Full textAbstract:
Population dynamics in the marine realm can shape species’ spatial structure and genetic variability between given geographical areas. Connectivity is an important factor of species’ population structure. In this study, we examined the genetic diversity and structure of white seabream (Diplodus sargus, L. 1758) in the eastern Mediterranean basin, using a panel of four microsatellite markers. Recorded low FST values within the study area indicate little evidence of genetic differentiation among populations. Results suggest high gene flow which may imply near-panmixia between populations, indicating the possibility of a probable movement of adult migrants, or strong passive drift at sea in early life stages of the species. To this extent, bibliographically speaking, different species within the Sparidae family favor altered population dynamics patterns with respect to local populations and genetic divergence, in the context of the molecular marker used.